Comment by inferiorhuman

With the original Arduino Due there was some fun undocumented behavior with the MCU (an Atmel Cortex-M3) where it would do random things at boot unless you installed a 10k resistor. From booting off of flash or ROM at random to clocks not coming up correctly.

I swear I was doing just fine with it booting reliably until I decided to try flashing it over the SWD interface. But wouldn't you know it, soldering a resistor fixed it. Mostly.